BERT is a powerful workflow for the automated deimmunization of proteins. BERT is based on three modular tools: EvoCS, MHCBoost or alternatively NetMHCIIPan and CoReM. Please refer to our wiki for details: Software.
Quick Setup for users
$ git clone https://github.com/steffenlem/Deimmunization
$ python setup.py install
- Installation of NetMHCIIpan (http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan)
We are unfortunately not allowed to ship NetMHCIIPan, but for academic users it's free of charge. If you have any issues with the setup, please don't hesitate to contact us on email@example.com .
The CLI - Command Line Interface
$ deimmunization --help Options: -in, --input_msa <arg> file path to msa.txt [required] -rs, --reference_sequence <arg> titlestring of reference sequence [required] -t, --majority_threshold <val> value between 0 and 1 to decide the consensus value [required] -a, --mhc_alleles <arg> Input the MHC allele in the following form: MHC-I: e.g. XXX-000 MHC-II: e.g. DRB1_0101 It is also possible (and recommended) to choose multiple alleles. The alleles have to be comma separated. e.g.; DRB1_0101, DRB1_0202, DRB1_0303, ... [required] -mp, --mhc_ii_pan <arg> path to netMHCIIpan [required] -mt, --number_mutations <val> the number of mutation which should be introduced in the sequence [required] -pos, --pos_to_check <val> the number of positions to check to introduce a mutation in each iteration [required] -pdb, --pdb_file <arg> path to pdb file [required] -cha, --pdb_chain <arg> Chain in the pdb file [required] -w, --weight <val> Weighting factor between deimmunization and ddG. A low value favors low immunity and a high valuefavors a stable protein [required] -frq, --allele_frequency <val> Frequency of the alleles in the target population. The frequencies have to be comma separated [required] --help Show this message and exit.
BERT -in <MSApath> -rs <ref.seqMSA> -t 0.5 -a DRB1_0301,DRB1_0701,DRB1_1501 -mp <path_netMHCIIPan> -pdb <path.pdb> -pos 2 -mt 2 -cha B -w 10 -frq 0.099,0.109,0.0967
You can use the following MSA, PDB and sequence files shipped with this program:
Example MSA: 'data/Isomerase_90_similarity.clustal_num'
Example PDB: 'data/2wcv.pdb'
Example Reference Sequence: '2WCV_Paris'
Performance and Results
BERT has been applied to team iGEM Paris-Bettencourt's FucU isomerase protein. The results are documented on our wiki: Collaboration. Moreover, BERT was used to deimmunize BoNTC. Details can be found on our software page: Software.
Our tool is made available under the MIT License.
Team iGEM 2018 Tübingen